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- PDB-1jc6: SOLUTION STRUCTURE OF BUNGARUS FACIATUS IX, A KUNITZ-TYPE CHYMOTR... -

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Basic information

Entry
Database: PDB / ID: 1jc6
TitleSOLUTION STRUCTURE OF BUNGARUS FACIATUS IX, A KUNITZ-TYPE CHYMOTRYPSIN INHIBITOR
ComponentsVENOM BASIC PROTEASE INHIBITORS IX AND VIIIB
KeywordsTOXIN / snake venom / Kunitz inhibitor / protease inhibitor / neurotoxin / solution structure / BF IX / Chymotrypsin Inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / toxin activity / extracellular region
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Kunitz-type serine protease inhibitor IX
Similarity search - Component
Biological speciesBungarus fasciatus (banded krait)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, C. / Hsu, C.H. / Su, N.Y. / Chiou, S.H. / Wu, S.H.
Citation
Journal: J.BIOL.CHEM. / Year: 2001
Title: Solution structure of a Kunitz-type chymotrypsin inhibitor isolated from the elapid snake Bungarus fasciatus
Authors: Chen, C. / Hsu, C.H. / Su, N.Y. / Lin, Y.C. / Chiou, S.H. / Wu, S.H.
#1: Journal: INT.J.PEPT.PROTEIN RES. / Year: 1983
Title: Complete amino acid sequences of two protease inhibitors in the venom of Bungarus fasciatus
Authors: Liu, C.S. / Wu, T.C. / Lo, T.B.
History
DepositionJun 8, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VENOM BASIC PROTEASE INHIBITORS IX AND VIIIB


Theoretical massNumber of molelcules
Total (without water)7,3051
Polymers7,3051
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 90The submitted conformer models are the 10 structures with the lowest
RepresentativeModel #1lowest energy

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Components

#1: Protein VENOM BASIC PROTEASE INHIBITORS IX AND VIIIB


Mass: 7305.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bungarus fasciatus (banded krait) / Tissue: VENOM / References: UniProt: P25660

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM BF IX; 50mM phosphate buffer NA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13.0 1 atm310 K
23.0 1 atm300 K
33.88 1 atm310 K
43.88 1 atm300 K
57.0 1 atm310 K
67.0 1 atm300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Karlsruheprocessing
AURELIA2.1.3Karlsruhedata analysis
X-PLOR98Brungerstructure solution
X-PLOR98Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 599 restraints, 536 are NOE-derived distance constraints, 33 dihedral angle restraints, 30 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: The submitted conformer models are the 10 structures with the lowest
Conformers calculated total number: 90 / Conformers submitted total number: 10

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